40Investigating the determinants of immunotherapy response in the primary tumor of clear cell renal cell carcinoma (RCC)

Abstract Background While previous studies have examined the determinants of a patient’s overall response to immune checkpoint inhibitor (ICI) in advanced RCC, the factors that specifically influence ICI response in the primary tumor remain poorly defined. This is of particular importance in the current era, where cytoreductive nephrectomy is less commonly performed, and many patients with metastatic disease still have the primary RCC tumor in place. To deepen our understanding of ICI response in the primary tumor and to understand the evolution of RCC on ICI, we conducted a comprehensive genomic analysis of paired pre- and post-treatment primary RCC tumors treated with ICI. Methods 46 RCC tissue samples comprised of 15 pre-treatment (biopsy of kidney) and 31 post-treatment nephrectomy samples (n = 33 patients, n = 13 with paired samples) were analyzed. 17 samples were from responders (30% radiographic shrinkage or ypT0, n = 4 pre-treatment, n = 13 post-treatment) and 29 samples were from non-responders (30% shrinkage, n = 11 pre-treatment, n = 18 post-treatment). Whole-exome and RNA-seq were performed at Caris Life Science. Wilcoxon rank-sum test was used to compare total mutation burden (TMB), loss of heterozygosity (LOH), and HLA evolutionary divergence (HED). Fisher’s exact test was used to assess the prevalence of driver genes for genes mutated in more than 3 samples. Comparisons were made between pre- and post-treatment specimens, and between response and nonresponse in pre-treatment samples. Ranked gene set enrichment analysis (GSEA) was performed using the 50 hallmark gene sets. Published immune signatures were quantified using single-sample GSEA. P-values were FDR adjusted, with a significance threshold at 0.05. Results Pre-treatment tumors that responded to ICI were significantly enriched for gene expression signatures of immune response, including interferon-alpha and interferon-gamma. Conversely, pre-treatment tumors resistant to ICI were significantly enriched for pathways associated with hypoxia, epithelial-to-mesenchymal transition, and metabolic activity. Further, pre-treatment responder biopsies are enriched for immune-related gene programs, including B cell and tertiary lymphoid structure (TLS) signatures compared to non-responder biopsies. Longitudinal analysis of paired samples reveals that immune pathways decline in responders and increase in non-responders post-treatment, suggesting divergent remodeling of the tumor microenvironment. These findings highlight the value of primary tumor profiling in understanding ICI response dynamics in RCC. Conclusions This study has important implications for understanding ICI response and resistance in the metastatic context, especially where the primary tumor remains in place, and in the neoadjuvant setting. Our findings suggest that that both the baseline immune landscape and treatment-induced transcriptional remodeling shape ICI response in primary RCC, and that the primary tumor provides a valuable window into these dynamics.